Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: VQJV1

Calculation Name: 3BZB-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BZB

Chain ID: B

ChEMBL ID:

UniProt ID: D0VWS8

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2277852.122366
FMO2-HF: Nuclear repulsion 2200413.613907
FMO2-HF: Total energy -77438.508459
FMO2-MP2: Total energy -77665.599294


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(B:29:ARG)


Summations of interaction energy for fragment #1(B:29:ARG)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-120.982-118.07620.848-11.108-12.645-0.114
Interaction energy analysis for fragmet #1(B:29:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.904 / q_NPA : 0.935
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3B31GLU-1-0.856-0.8931.703-107.849-109.83218.784-8.195-8.606-0.091
4B32ARG10.9120.9414.16330.12330.2310.000-0.033-0.0750.000
5B33TYR0-0.017-0.0557.947-2.771-2.7710.0000.0000.0000.000
6B34GLN00.0220.04310.6920.6620.6620.0000.0000.0000.000
7B35SER00.0590.04214.295-0.514-0.5140.0000.0000.0000.000
8B36PRO0-0.031-0.00916.4670.3130.3130.0000.0000.0000.000
9B37ALA00.0280.01418.4370.7330.7330.0000.0000.0000.000
10B38GLY0-0.013-0.00821.3270.2520.2520.0000.0000.0000.000
11B39ALA0-0.037-0.00521.4050.4940.4940.0000.0000.0000.000
12B40PRO00.0040.00223.3690.0240.0240.0000.0000.0000.000
13B41LEU0-0.0080.01920.5450.2680.2680.0000.0000.0000.000
14B42GLN0-0.075-0.05820.924-1.022-1.0220.0000.0000.0000.000
15B43CYS0-0.027-0.01518.0890.0990.0990.0000.0000.0000.000
16B44SER0-0.020-0.03714.708-0.319-0.3190.0000.0000.0000.000
17B45VAL00.0000.00310.8400.5150.5150.0000.0000.0000.000
18B46GLN0-0.030-0.0198.375-1.849-1.8490.0000.0000.0000.000
19B47VAL00.0080.0156.5662.0312.0310.0000.0000.0000.000
20B48GLN0-0.032-0.0264.793-6.698-6.551-0.001-0.023-0.1220.000
21B49THR0-0.034-0.0152.1390.5572.6211.530-1.383-2.211-0.003
22B50THR00.0160.0132.570-11.003-8.4330.535-1.474-1.631-0.020
23B62SER0-0.030-0.0347.392-0.269-0.2690.0000.0000.0000.000
24B63GLY00.037-0.0039.0242.0362.0360.0000.0000.0000.000
25B64ALA00.0160.0049.7171.5321.5320.0000.0000.0000.000
26B65ARG10.8160.8905.31042.16342.1630.0000.0000.0000.000
27B66ALA00.0670.03911.0641.5771.5770.0000.0000.0000.000
28B67LEU0-0.0100.01114.2251.5881.5880.0000.0000.0000.000
29B68ALA00.0450.02113.4381.2191.2190.0000.0000.0000.000
30B69ASP-1-0.772-0.88214.064-20.157-20.1570.0000.0000.0000.000
31B70THR0-0.090-0.05316.6301.3151.3150.0000.0000.0000.000
32B71LEU0-0.015-0.00718.2390.8380.8380.0000.0000.0000.000
33B72CYS0-0.046-0.01717.5020.4980.4980.0000.0000.0000.000
34B73TRP0-0.023-0.02719.7580.8990.8990.0000.0000.0000.000
35B74GLN0-0.073-0.03422.7220.4130.4130.0000.0000.0000.000
36B75PRO00.0620.03524.211-0.057-0.0570.0000.0000.0000.000
37B76GLU-1-0.839-0.92725.422-11.226-11.2260.0000.0000.0000.000
38B77LEU0-0.080-0.03123.2680.2380.2380.0000.0000.0000.000
39B78ILE0-0.048-0.02622.1730.0070.0070.0000.0000.0000.000
40B79ALA00.0110.02526.4270.1130.1130.0000.0000.0000.000
41B80GLY0-0.047-0.02528.3830.3530.3530.0000.0000.0000.000
42B81LYS10.8030.90528.59110.43510.4350.0000.0000.0000.000
43B82THR00.0330.03627.878-0.518-0.5180.0000.0000.0000.000
44B83VAL0-0.011-0.02722.172-0.018-0.0180.0000.0000.0000.000
45B84CYS0-0.057-0.02322.496-0.062-0.0620.0000.0000.0000.000
46B85GLU-1-0.804-0.88314.863-20.002-20.0020.0000.0000.0000.000
47B86LEU0-0.0160.00519.1460.2230.2230.0000.0000.0000.000
48B87GLY0-0.006-0.00615.931-0.489-0.4890.0000.0000.0000.000
49B88ALA00.0110.00713.830-1.290-1.2900.0000.0000.0000.000
50B89GLY00.0360.02110.499-1.734-1.7340.0000.0000.0000.000
51B90ALA0-0.030-0.0127.2420.2260.2260.0000.0000.0000.000
52B91GLY00.0600.0129.2811.0551.0550.0000.0000.0000.000
53B92LEU0-0.039-0.0149.4431.1391.1390.0000.0000.0000.000
54B93VAL00.0010.00212.2001.1521.1520.0000.0000.0000.000
55B94SER00.021-0.02915.3061.5371.5370.0000.0000.0000.000
56B95ILE0-0.049-0.01012.7911.0541.0540.0000.0000.0000.000
57B96VAL0-0.008-0.01615.1230.8680.8680.0000.0000.0000.000
58B97ALA00.017-0.00517.7310.9010.9010.0000.0000.0000.000
59B98PHE0-0.016-0.01420.0760.8020.8020.0000.0000.0000.000
60B99LEU0-0.031-0.01917.4530.6020.6020.0000.0000.0000.000
61B100ALA0-0.014-0.00121.4850.4660.4660.0000.0000.0000.000
62B101GLY0-0.0100.00123.6460.5330.5330.0000.0000.0000.000
63B102ALA0-0.0050.00924.3770.4890.4890.0000.0000.0000.000
64B103ASP-1-0.942-0.97926.343-10.268-10.2680.0000.0000.0000.000
65B104GLN0-0.057-0.03726.352-0.074-0.0740.0000.0000.0000.000
66B105VAL00.0220.01220.425-0.135-0.1350.0000.0000.0000.000
67B106VAL0-0.008-0.00522.1640.0850.0850.0000.0000.0000.000
68B107ALA00.0820.05416.713-0.192-0.1920.0000.0000.0000.000
69B108THR0-0.070-0.06218.5260.6790.6790.0000.0000.0000.000
70B109ASP-1-0.783-0.90113.996-21.276-21.2760.0000.0000.0000.000
71B110TYR00.0370.02416.7321.5171.5170.0000.0000.0000.000
72B111PRO0-0.041-0.02316.918-0.416-0.4160.0000.0000.0000.000
73B112ASP-1-0.847-0.92712.916-18.418-18.4180.0000.0000.0000.000
74B113PRO0-0.014-0.00414.924-0.300-0.3000.0000.0000.0000.000
75B114GLU-1-0.862-0.9268.974-19.593-19.5930.0000.0000.0000.000
76B115ILE0-0.028-0.0089.905-1.541-1.5410.0000.0000.0000.000
77B116LEU0-0.027-0.01211.230-0.145-0.1450.0000.0000.0000.000
78B117ASN0-0.012-0.00711.5870.8470.8470.0000.0000.0000.000
79B118SER0-0.031-0.0237.477-0.386-0.3860.0000.0000.0000.000
80B119LEU0-0.0050.0139.458-0.045-0.0450.0000.0000.0000.000
81B120GLU-1-0.840-0.91311.796-14.015-14.0150.0000.0000.0000.000
82B121SER0-0.020-0.0139.9320.6020.6020.0000.0000.0000.000
83B122ASN00.009-0.0047.7910.3210.3210.0000.0000.0000.000
84B123ILE0-0.008-0.00911.6130.4860.4860.0000.0000.0000.000
85B124ARG10.8110.88014.88816.11816.1180.0000.0000.0000.000
86B125GLU-1-0.948-0.94911.212-20.119-20.1190.0000.0000.0000.000
87B126HIS0-0.046-0.01511.876-0.190-0.1900.0000.0000.0000.000
88B138ARG10.9790.97928.3459.2899.2890.0000.0000.0000.000
89B139ALA0-0.022-0.01427.253-0.142-0.1420.0000.0000.0000.000
90B140SER00.0310.02521.740-0.031-0.0310.0000.0000.0000.000
91B141PRO0-0.004-0.00619.2610.3190.3190.0000.0000.0000.000
92B142LYS10.8970.95620.50111.20911.2090.0000.0000.0000.000
93B143VAL00.0350.02516.076-0.429-0.4290.0000.0000.0000.000
94B144VAL0-0.038-0.03019.1150.7260.7260.0000.0000.0000.000
95B145PRO00.003-0.00219.534-0.429-0.4290.0000.0000.0000.000
96B146TYR0-0.051-0.05720.2310.6540.6540.0000.0000.0000.000
97B147ARG10.8420.91921.00011.54511.5450.0000.0000.0000.000
98B148TRP00.044-0.00116.9720.6860.6860.0000.0000.0000.000
99B149GLY0-0.0170.00023.7530.1290.1290.0000.0000.0000.000
100B150ASP-1-0.785-0.86226.697-10.950-10.9500.0000.0000.0000.000
101B151SER0-0.0060.00128.5950.0200.0200.0000.0000.0000.000
102B152PRO00.0380.00928.093-0.075-0.0750.0000.0000.0000.000
103B153ASP-1-0.814-0.87529.095-9.115-9.1150.0000.0000.0000.000
104B154SER00.0160.00526.5770.1470.1470.0000.0000.0000.000
105B155LEU00.0560.02424.2710.0600.0600.0000.0000.0000.000
106B156GLN0-0.0300.01027.1990.2320.2320.0000.0000.0000.000
107B157ARG10.8450.87930.7359.2839.2830.0000.0000.0000.000
108B158CYS0-0.071-0.02025.8210.0500.0500.0000.0000.0000.000
109B159THR0-0.039-0.04426.010-0.147-0.1470.0000.0000.0000.000
110B160GLY00.0050.02128.7540.1060.1060.0000.0000.0000.000
111B161LEU0-0.028-0.00628.8870.2330.2330.0000.0000.0000.000
112B162GLN0-0.010-0.01331.170-0.253-0.2530.0000.0000.0000.000
113B163ARG10.8500.92730.5899.3419.3410.0000.0000.0000.000
114B164PHE00.0300.02126.9600.1000.1000.0000.0000.0000.000
115B165GLN0-0.017-0.01729.020-0.025-0.0250.0000.0000.0000.000
116B166VAL00.0040.00923.6140.0490.0490.0000.0000.0000.000
117B167VAL0-0.0160.00022.807-0.136-0.1360.0000.0000.0000.000
118B168LEU00.0100.00218.6490.0270.0270.0000.0000.0000.000
119B169LEU00.0190.00518.328-0.172-0.1720.0000.0000.0000.000
120B170ALA00.0630.02613.3170.2560.2560.0000.0000.0000.000
121B171ASP-1-0.737-0.86310.932-26.560-26.5600.0000.0000.0000.000
122B172LEU0-0.037-0.00814.0590.1540.1540.0000.0000.0000.000
123B173LEU0-0.024-0.00416.5940.7040.7040.0000.0000.0000.000
124B174SER0-0.0240.00414.5060.8020.8020.0000.0000.0000.000
125B175PHE00.0260.01016.7020.1680.1680.0000.0000.0000.000
126B176HIS00.045-0.00719.4610.2260.2260.0000.0000.0000.000
127B177GLN0-0.0060.00823.0280.6140.6140.0000.0000.0000.000
128B178ALA0-0.0070.00721.4300.3740.3740.0000.0000.0000.000
129B179HIS0-0.051-0.03620.8890.6090.6090.0000.0000.0000.000
130B180ASP-1-0.772-0.87124.794-10.592-10.5920.0000.0000.0000.000
131B181ALA00.0230.02224.4190.1890.1890.0000.0000.0000.000
132B182LEU00.0010.02620.2140.1990.1990.0000.0000.0000.000
133B183LEU00.0070.00824.4360.1420.1420.0000.0000.0000.000
134B184ARG10.7950.85827.73110.94810.9480.0000.0000.0000.000
135B185SER00.016-0.01125.0180.1750.1750.0000.0000.0000.000
136B186VAL00.0080.00725.1320.1840.1840.0000.0000.0000.000
137B187LYS10.7840.88027.5289.6859.6850.0000.0000.0000.000
138B188MET0-0.056-0.02729.9780.3880.3880.0000.0000.0000.000
139B189LEU00.0280.01824.8640.2340.2340.0000.0000.0000.000
140B190LEU0-0.0140.01228.3050.0440.0440.0000.0000.0000.000
141B191ALA00.010-0.00430.0020.4090.4090.0000.0000.0000.000
142B192LEU00.0370.02132.9010.0210.0210.0000.0000.0000.000
143B193PRO00.027-0.00636.2240.0870.0870.0000.0000.0000.000
144B194ALA0-0.045-0.02337.9840.1280.1280.0000.0000.0000.000
145B195ASN0-0.058-0.02037.2920.2410.2410.0000.0000.0000.000
146B196ASP-1-0.706-0.85933.265-9.526-9.5260.0000.0000.0000.000
147B197PRO0-0.047-0.01935.366-0.203-0.2030.0000.0000.0000.000
148B198THR0-0.066-0.02732.428-0.009-0.0090.0000.0000.0000.000
149B199ALA0-0.0020.02430.922-0.310-0.3100.0000.0000.0000.000
150B200VAL0-0.051-0.03126.5480.1310.1310.0000.0000.0000.000
151B201ALA00.0180.01324.788-0.224-0.2240.0000.0000.0000.000
152B202LEU00.0070.00821.7020.1540.1540.0000.0000.0000.000
153B203VAL00.010-0.00119.970-0.521-0.5210.0000.0000.0000.000
154B204THR0-0.037-0.02015.4060.2380.2380.0000.0000.0000.000
155B205PHE0-0.014-0.00315.021-0.714-0.7140.0000.0000.0000.000
156B206THR0-0.007-0.01210.3740.1870.1870.0000.0000.0000.000
157B207HIS0-0.076-0.04113.5150.1950.1950.0000.0000.0000.000
158B208HIS00.0400.02210.5130.4630.4630.0000.0000.0000.000
159B209ARG10.8050.87615.74415.58615.5860.0000.0000.0000.000
160B210PRO0-0.0040.00719.477-0.162-0.1620.0000.0000.0000.000
161B211HIS00.0320.01121.9040.3680.3680.0000.0000.0000.000
162B212LEU0-0.037-0.01020.986-0.362-0.3620.0000.0000.0000.000
163B213ALA00.0110.00523.4780.6060.6060.0000.0000.0000.000
164B214GLU-1-0.822-0.90425.290-10.487-10.4870.0000.0000.0000.000
165B215ARG00.0230.02622.213-0.095-0.0950.0000.0000.0000.000
166B216ASP-1-0.729-0.85421.113-14.684-14.6840.0000.0000.0000.000
167B217LEU00.0200.01021.803-0.390-0.3900.0000.0000.0000.000
168B218ALA0-0.035-0.01424.5160.4160.4160.0000.0000.0000.000
169B219PHE00.0410.02923.2170.3880.3880.0000.0000.0000.000
170B220PHE00.0680.01721.5520.4160.4160.0000.0000.0000.000
171B221ARG10.8230.90527.06711.01311.0130.0000.0000.0000.000
172B222LEU00.0200.01528.0490.3760.3760.0000.0000.0000.000
173B223VAL0-0.035-0.03126.9900.3200.3200.0000.0000.0000.000
174B224ASN0-0.020-0.01330.2340.3990.3990.0000.0000.0000.000
175B225ALA0-0.0290.00432.9250.3250.3250.0000.0000.0000.000
176B226ASP-1-0.792-0.87633.078-9.032-9.0320.0000.0000.0000.000
177B227GLY00.0500.01634.690-0.120-0.1200.0000.0000.0000.000
178B228ALA0-0.070-0.02635.0560.1590.1590.0000.0000.0000.000
179B229LEU0-0.043-0.02629.721-0.030-0.0300.0000.0000.0000.000
180B230ILE00.0050.01732.2940.1410.1410.0000.0000.0000.000
181B231ALA0-0.013-0.01927.686-0.354-0.3540.0000.0000.0000.000
182B232GLU-1-0.745-0.82028.280-9.748-9.7480.0000.0000.0000.000
183B233PRO00.0120.00025.840-0.439-0.4390.0000.0000.0000.000
184B234TRP0-0.035-0.00920.5710.2900.2900.0000.0000.0000.000
185B235LEU00.0220.00422.7120.2830.2830.0000.0000.0000.000
186B236SER00.0170.01523.864-0.186-0.1860.0000.0000.0000.000
187B237PRO00.0200.00719.683-0.403-0.4030.0000.0000.0000.000
188B238LEU0-0.0110.01016.4690.4170.4170.0000.0000.0000.000
189B239GLN00.0300.00216.296-0.158-0.1580.0000.0000.0000.000
190B240MET0-0.0050.02411.449-0.370-0.3700.0000.0000.0000.000
191B256GLN0-0.022-0.01814.6810.5730.5730.0000.0000.0000.000
192B257VAL0-0.020-0.01912.545-0.971-0.9710.0000.0000.0000.000
193B258HIS00.0010.00015.6061.1661.1660.0000.0000.0000.000
194B259ARG10.8950.92218.44514.27814.2780.0000.0000.0000.000
195B260TRP00.0150.00120.9390.9000.9000.0000.0000.0000.000
196B261ARG10.8530.91023.14610.31810.3180.0000.0000.0000.000
197B262LEU00.0010.00324.9740.2940.2940.0000.0000.0000.000
198B263ARG10.8580.90428.0369.4499.4490.0000.0000.0000.000
199B264TRP0-0.006-0.00431.3840.1770.1770.0000.0000.0000.000
200B265ARG10.9350.97834.7998.3238.3230.0000.0000.0000.000